- PDB-3ffi: HIV-1 RT with pyridone non-nucleoside inhibitor -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ffi
Title
HIV-1 RT with pyridone non-nucleoside inhibitor
Components
RT p51
Reverse transcriptase/ribonuclease H
Keywords
TRANSFERASE / HIV / RT / REVERSE TRANSCRIPTASE / TRANSFERASE RNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / AIDS / Cytoplasm / Viral nucleoprotein / Hydrolase
Function / homology
Function and homology information
integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.6→2.69 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.23 / Num. unique all: 551 / Rsym value: 0.293 / % possible all: 13.1
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→46.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.402 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28453
1660
5.2 %
RANDOM
Rwork
0.23406
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-
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obs
0.23673
30250
74.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 70.794 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.69 Å2
0 Å2
0 Å2
2-
-
-1.01 Å2
0 Å2
3-
-
-
1.71 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→46.78 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7810
0
33
60
7903
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
8056
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
5567
X-RAY DIFFRACTION
r_angle_refined_deg
0.932
1.965
10951
X-RAY DIFFRACTION
r_angle_other_deg
0.738
3
13670
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.651
5
946
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.41
25.237
359
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.978
15
1460
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.063
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.054
0.2
1187
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
8683
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1484
X-RAY DIFFRACTION
r_nbd_refined
0.194
0.2
1845
X-RAY DIFFRACTION
r_nbd_other
0.169
0.2
5727
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
3895
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
4182
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.123
0.2
230
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.07
0.2
18
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.173
0.2
67
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.124
0.2
2
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.35
1.5
4969
X-RAY DIFFRACTION
r_mcbond_other
0.032
1.5
1894
X-RAY DIFFRACTION
r_mcangle_it
0.621
2
7798
X-RAY DIFFRACTION
r_scbond_it
0.436
3
3721
X-RAY DIFFRACTION
r_scangle_it
0.729
4.5
3153
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.6→2.668 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.354
13
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Rwork
0.353
292
-
obs
-
551
9.82 %
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